Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [89s/113s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(Colossus)
  > 
  > test_check("Colossus")
  Saving _problems/test-CaseControl-72.R
  Saving _problems/test-CaseControl-72.R
  Saving _problems/test-CaseControl-223.R
  Saving _problems/test-CaseControl-223.R
  Saving _problems/test-CaseControl-223.R
  Saving _problems/test-CaseControl-223.R
  Saving _problems/test-CaseControl-242.R
  Saving _problems/test-CaseControl-344.R
  Saving _problems/test-CaseControl-345.R
  Saving _problems/test-CaseControl-349.R
  Saving _problems/test-CaseControl-350.R
  Saving _problems/test-CaseControl-351.R
  Saving _problems/test-CaseControl-352.R
  Saving _problems/test-CaseControl-349.R
  Saving _problems/test-CaseControl-350.R
  Saving _problems/test-CaseControl-351.R
  Saving _problems/test-CaseControl-352.R
  Saving _problems/test-CaseControl-363.R
  Saving _problems/test-CaseControl-364.R
  Saving _problems/test-CaseControl-366.R
  Saving _problems/test-CoxPlot-154.R
  Saving _problems/test-CoxRegression-118.R
  Saving _problems/test-CoxRegression-163.R
  Saving _problems/test-Formula-176.R
  Saving _problems/test-Gradient-63.R
  Saving _problems/test-Gradient-135.R
  Saving _problems/test-Norm-58.R
  Saving _problems/test-Norm-61.R
  Saving _problems/test-Norm-58.R
  Saving _problems/test-Norm-61.R
  Saving _problems/test-Norm-67.R
  Saving _problems/test-Norm-67.R
  Saving _problems/test-Omnibus-366.R
  Saving _problems/test-Utility-170.R
  Saving _problems/test-Utility-171.R
  [ FAIL 35 | WARN 12 | SKIP 15 | PASS 825 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • Cran Skip (15): 'test-Assigned.R:74:5', 'test-CoxRegression.R:215:5',
    'test-Logbound.R:24:5', 'test-Logbound.R:110:5', 'test-Logbound.R:161:5',
    'test-Logbound.R:203:5', 'test-Logbound.R:251:5', 'test-Logbound.R:329:5',
    'test-Logbound.R:357:5', 'test-Omnibus.R:21:5', 'test-Omnibus.R:67:5',
    'test-Omnibus.R:147:5', 'test-Omnibus.R:214:5', 'test-Omnibus.R:256:5',
    'test-Omnibus.R:453:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-CaseControl.R:72:11'): threshold nonfail ─────────────────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 850.9
  `expected`: 847.1
  
  ── Failure ('test-CaseControl.R:72:11'): threshold nonfail ─────────────────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 62.1
  `expected`: 63.5
  
  ── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 1001.9
  `expected`: 2365.3
  
  ── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 620.3
  `expected`: 645.8
  
  ── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 732.7
  `expected`: 662.9
  
  ── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 898.3
  `expected`: 645.8
  
  ── Failure ('test-CaseControl.R:242:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 962.7
  `expected`: 961.7
  
  ── Failure ('test-CaseControl.R:344:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model0_sde[i_index]`.
  Differences:
    `actual`: 0.01406
  `expected`: 0.01403
  
  ── Failure ('test-CaseControl.R:345:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model0_sde[i_index + 1]`.
  Differences:
    `actual`: 0.4912
  `expected`: 0.4901
  
  ── Failure ('test-CaseControl.R:349:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[1]` to equal `model1_sdo[i_index]`.
  Differences:
    `actual`: 0.0161
  `expected`: 0.0138
  
  ── Failure ('test-CaseControl.R:350:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[2]` to equal `model1_sdo[i_index + 1]`.
  Differences:
    `actual`: 0.371
  `expected`: 0.432
  
  ── Failure ('test-CaseControl.R:351:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model1_sde[i_index]`.
  Differences:
    `actual`: 0.01353
  `expected`: 0.01406
  
  ── Failure ('test-CaseControl.R:352:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model1_sde[i_index + 1]`.
  Differences:
    `actual`: 0.48189
  `expected`: 0.48225
  
  ── Failure ('test-CaseControl.R:349:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[1]` to equal `model1_sdo[i_index]`.
  Differences:
    `actual`: 0.0164
  `expected`: 0.0232
  
  ── Failure ('test-CaseControl.R:350:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[2]` to equal `model1_sdo[i_index + 1]`.
  Differences:
    `actual`: 0.36
  `expected`: 0.51
  
  ── Failure ('test-CaseControl.R:351:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model1_sde[i_index]`.
  Differences:
    `actual`: 0.0164
  `expected`: 0.0232
  
  ── Failure ('test-CaseControl.R:352:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model1_sde[i_index + 1]`.
  Differences:
    `actual`: 0.36
  `expected`: 0.51
  
  ── Failure ('test-CaseControl.R:363:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[1]` to equal `model3_sdo[i_index]`.
  Differences:
    `actual`: 0.0039
  `expected`: 0.0056
  
  ── Failure ('test-CaseControl.R:364:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[2]` to equal `model3_sdo[i_index + 1]`.
  Differences:
    `actual`: 0.114
  `expected`: 0.161
  
  ── Failure ('test-CaseControl.R:366:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model3_sde[i_index + 1]`.
  Differences:
    `actual`: 0.16085
  `expected`: 0.16083
  
  ── Failure ('test-CoxPlot.R:154:5'): Coxph risk plotting above discrete step number limit ──
  Expected `ep$y[100]` to equal 0.9938494.
  Differences:
    `actual`: 0.976
  `expected`: 0.994
  
  ── Failure ('test-CoxRegression.R:118:3'): Coxph dose list ─────────────────────
  Expected `e$beta_0` to equal `c(...)`.
  Differences:
       actual | expected               
   [1] 1.000  | 1.000    [1]           
   [2] -0.037 - -0.088   [2]           
   [3] -0.065 - -0.090   [3]           
   [4] 0.598  - 0.991    [4]           
   [5] -0.120 - -0.053   [5]           
   [6] 1.126  - 1.119    [6]           
   [7] 3.057  - 2.942    [7]           
   [8] 0.175  - 0.107    [8]           
   [9] 0.232  - 1.573    [9]           
  [10] 0.300  - 0.301    [10]          
   ... ...      ...      and 2 more ...
  
  ── Failure ('test-CoxRegression.R:163:3'): Coxph loglin_M Null ─────────────────
  Expected `e$AIC` to equal 1052.
  Differences:
    `actual`: 2103.1
  `expected`: 1052.0
  
  ── Failure ('test-Formula.R:176:3'): Checking formula works with result modification ──
  Expected `sum(f$Risk)` to equal 548.6874.
  Differences:
    `actual`: 858.2
  `expected`: 548.7
  
  ── Failure ('test-Gradient.R:63:3'): Coxph gradient methods ────────────────────
  Expected `e2$beta_0` to equal `c(0.6594536, 0.7276018)`.
  Differences:
    `actual`: 0.6585 0.7271
  `expected`: 0.6595 0.7276
  
  ── Failure ('test-Gradient.R:135:5'): Constraint Check ─────────────────────────
  Expected `e4$beta_0` to equal `c(0.04037, -0.04037)`.
  Differences:
    `actual`: 0.0402 -0.0402
  `expected`: 0.0404 -0.0404
  
  ── Failure ('test-Norm.R:58:7'): Checking values converted back ────────────────
  Expected `res$First_Der` to equal `res_max$First_Der`.
  Differences:
    `actual`: 3218.9 -15.2
  `expected`: 1609.4  -7.6
  
  ── Failure ('test-Norm.R:61:7'): Checking values converted back ────────────────
  Expected `res$Second_Der` to equal `res_max$Second_Der`.
  Differences:
  actual vs expected
                          [,1]      [,2]
  - actual[1, ]   -30854.26606 -26.77289
  + expected[1, ] -15427.13303 -13.38645
  - actual[2, ]      -26.77289 -38.54087
  + expected[2, ]    -13.38645 -19.27044
  
  ── Failure ('test-Norm.R:58:7'): Checking values converted back ────────────────
  Expected `res$First_Der` to equal `res_max$First_Der`.
  Differences:
    `actual`: -15.6  -6.4
  `expected`: -31.3 -12.8
  
  ── Failure ('test-Norm.R:61:7'): Checking values converted back ────────────────
  Expected `res$Second_Der` to equal `res_max$Second_Der`.
  Differences:
  actual vs expected
                          [,1]      [,2]
  - actual[1, ]   -32778.82740  15.26637
  + expected[1, ] -65557.65480  30.53274
  - actual[2, ]       15.26637 -24.61536
  + expected[2, ]     30.53274 -49.23072
  
  ── Failure ('test-Norm.R:67:7'): Checking values converted back ────────────────
  Expected `res$Standard_Deviation` to equal `res_max$Standard_Deviation`.
  Differences:
    `actual`: 0.006 0.202
  `expected`: 0.004 0.143
  
  ── Failure ('test-Norm.R:67:7'): Checking values converted back ────────────────
  Expected `res$Standard_Deviation` to equal `res_max$Standard_Deviation`.
  Differences:
    `actual`: 0.007 0.203
  `expected`: 0.005 0.144
  
  ── Failure ('test-Omnibus.R:366:3'): check deviation calc, expected cox ────────
  Expected `devs` to equal `c(...)`.
  Differences:
    `actual`: 0.43448 0.38255 0.52225 0.67186 0.45005 0.56292 0.73815 0.97195
  `expected`: 0.61445 0.54101 0.73858 0.95015 0.63646 0.56292 0.73815 0.97195
  
  ── Failure ('test-Utility.R:170:3'): Improve Ratio test ────────────────────────
  Expected `val$Difference` to equal 2.200062.
  Differences:
    `actual`: 5.9
  `expected`: 2.2
  
  ── Failure ('test-Utility.R:171:3'): Improve Ratio test ────────────────────────
  Expected `val$"p value"` to equal 0.5319362.
  Differences:
    `actual`: 0.12
  `expected`: 0.53
  
  
  [ FAIL 35 | WARN 12 | SKIP 15 | PASS 825 ]
  Error:
  ! Test failures.
  Execution halted